ABCA12 p.Ile2053=
c.6159T>A · rs201569862 · VCV727997
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.196%, eas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 1.1 | GERP -3.2, phastCons 0.99 |
| Overall | ||
| CADD | 1.932 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.196%
East Asian · 88/44,824 alleles
Filtering AF
0.163%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.151%
Overall
0.00595%
96/1,613,782 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.196% | 509 |
| Remaining individualsnot grpmax-eligible | 0.0096% | 10,414 |
| Admixed American | 0.00333% | 30,005 |
Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.
Variant & gene context
- Gene
- ABCA12
- Protein
- p.Ile2053=
- Coding
- c.6159T>A
- MANE Select
- NM_173076
- dbSNP
- rs201569862
- Type
- single nucleotide variant
- Location
- chr2:214956737 (GRCh38)
- Gene constraint
- LOEUF 0.582 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 68.32
- Residue 2053
- a UniProt-annotated variant site (in arci4b); a UniProt-annotated variant site (in arci4b; uncertain significance)
Similar variants
- ABCA12 p.Ile2053Val Uncertain significance ★ ⚠ same residue
- ABCA12 c.2592+1G>A Likely pathogenic ★★ same type
- ABCA12 c.5381+1G>C Pathogenic/Likely pathogenic ★★ same type
- ABCA12 c.985+1G>A Likely pathogenic ★★ same type
- ABCA12 p.Arg1297Ter Pathogenic ★★ same type
- ABCA12 p.Arg1514Cys Pathogenic ★★ same type
- ABCA12 p.Arg1514His Pathogenic/Likely pathogenic ★★ same type
- ABCA12 p.Arg1515Ter Pathogenic ★★ same type
Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →
Cite Sugi Variant
Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/abca12-p-ile2053 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown